chr13-66631255-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_203487.3(PCDH9):c.3295C>T(p.Pro1099Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,268 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1099L) has been classified as Likely benign.
Frequency
Consequence
NM_203487.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH9 | NM_203487.3 | c.3295C>T | p.Pro1099Ser | missense_variant | 4/5 | ENST00000377865.7 | |
LOC105370247 | XR_007063818.1 | n.169-28806G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH9 | ENST00000377865.7 | c.3295C>T | p.Pro1099Ser | missense_variant | 4/5 | 1 | NM_203487.3 | ||
PCDH9 | ENST00000544246.5 | c.3193C>T | p.Pro1065Ser | missense_variant | 3/4 | 1 | P1 | ||
PCDH9 | ENST00000456367.5 | c.3169C>T | p.Pro1057Ser | missense_variant | 4/5 | 1 | |||
PCDH9 | ENST00000614931.1 | c.*208C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251318Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135832
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458268Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 725738
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
PCDH9-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 26, 2023 | The PCDH9 c.3295C>T variant is predicted to result in the amino acid substitution p.Pro1099Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/13-67205387-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at